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LOC121725215 Sharpr-MPRA regulatory region 9285 [ Homo sapiens (human) ]

Gene ID: 121725215, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725215
Gene description
Sharpr-MPRA regulatory region 9285
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (115072672..115072966)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (115585850..115586145)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (114408369..114408663)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene potassium calcium-activated channel subfamily N member 2 Neighboring gene NANOG hESC enhancer GRCh37_chr5:113590875-113591386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:113613789-113614290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:113614291-113614790 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:113643487-113644315 Neighboring gene RN7SK pseudogene 89 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:113695880-113696796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16244 Neighboring gene NANOG hESC enhancer GRCh37_chr5:113724412-113724913 Neighboring gene uncharacterized LOC101927078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:113880373-113880872 Neighboring gene long intergenic non-protein coding RNA 1957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:114117551-114118374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:114118375-114119196 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114364005-114364746 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114364747-114365486 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:114368052-114369251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22923 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:114404076-114405275 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114426221-114426720 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:114426721-114427222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16247 Neighboring gene tripartite motif containing 36 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22926 Neighboring gene protein geranylgeranyltransferase type I subunit beta

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_075689.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    115072672..115072966
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    115585850..115586145
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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